rs10494554

Variant names:

• chr1-183146754-T-G
• rs10494554

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0893 in 152,228 control chromosomes in the GnomAD database, including 1,534 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.089 (1534 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.301
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0892 AC: 13568 AN: 152110 Hom.: 1529 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0634

Gnomad ASJ AF: 0.0156

Gnomad EAS AF: 0.230

Gnomad SAS AF: 0.0468

Gnomad FIN AF: 0.00348

Gnomad MID AF: 0.0475

Gnomad NFE AF: 0.00595

Gnomad OTH AF: 0.0764

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0893 AC: 13592 AN: 152228 Hom.: 1534 Cov.: 32 AF XY: 0.0892 AC XY: 6643 AN XY: 74448

African (AFR) AF: 0.254 AC: 10515 AN: 41478

American (AMR) AF: 0.0633 AC: 968 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0156 AC: 54 AN: 3470

East Asian (EAS) AF: 0.231 AC: 1195 AN: 5184

South Asian (SAS) AF: 0.0469 AC: 226 AN: 4820

European-Finnish (FIN) AF: 0.00348 AC: 37 AN: 10624

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.00595 AC: 405 AN: 68038

Other (OTH) AF: 0.0766 AC: 162 AN: 2116

Alfa AF: 0.0592 Hom.: 145

Bravo AF: 0.105

Asia WGS AF: 0.142 AC: 494 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	1.4
DANN	Benign	0.52
PhyloP100		-0.30

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10494554; hg19: chr1-183115889;